Package org.biojava.nbio.structure

Interface Structure

  • All Superinterfaces:
    Cloneable, Serializable
    All Known Implementing Classes:
    StructureImpl
    public interface Structure
extends Cloneable, Serializable
    Interface for a structure object. Provides access to the data of a PDB file. A structure object allows to access the PDB header information as well as to the data from the ATOM records. The header information is currently available through the following objects: The structure object provides access to the data from the ATOM records through a hierarchy of sub-object: 
     Structure
         |
         Chain
             |
             Group
                 |
                 Atom
    For more documentation on how to work with the Structure API please see http://biojava.org/wiki/BioJava:CookBook#Protein_Structure

    The tutorial for the BioJava structure modules can be found at github.

    Q: How can I get a Structure object from a PDB file?

    A: 

      Structure loadStructure(String pathToPDBFile){
                PDBFileReader pdbreader = new PDBFileReader();

                Structure structure = null;
                try{
                        structure = pdbreader.getStructure(pathToPDBFile);
                        System.out.println(structure);
                } catch (IOException e) {
                        e.printStackTrace();
                }
                return structure;
        }

    Q: How can I calculate Phi and Psi angles of AminoAcids?

    A: 

      void calcPhiPsi(Structure structure){


                // get the first chain from the structure

                Chain chain  = structure.getChain(0);

                // A protein chain consists of a number of groups. These can be either
                // AminoAcid, Hetatom or Nucleotide groups.
                //
                // Note: BioJava provides access to both the ATOM and SEQRES data in a PDB file.
                // since we are interested in doing calculations here, we only request the groups
                // from the ATOM records

                //  get the Groups of the chain that are AminoAcids.
                List groups = chain.getAtomGroups(GroupType.AMINOACID);

                AminoAcid a;
                AminoAcid b;
                AminoAcid c ;

                for ( int i=0; i < groups.size(); i++){

                        // since we requested only groups of type AMINOACID they will always be amino acids
                        // Nucleotide and Hetatom groups will not be present in the groups list.

                        b = (AminoAcid)groups.get(i);

                        double phi =360.0;
                        double psi =360.0;

                        if ( i > 0) {
                                a = (AminoAcid)groups.get(i-1) ;
                                try {

                                        // the Calc class provides utility methods for various calculations on
                                        // structures, groups and atoms

                                        phi = Calc.getPhi(a,b);
                                } catch (StructureException e){
                                        e.printStackTrace();
                                        phi = 360.0 ;
                                }
                        }
                        if ( i < groups.size()-1) {
                                c = (AminoAcid)groups.get(i+1) ;
                                try {
                                        psi = Calc.getPsi(b,c);
                                }catch (StructureException e){
                                        e.printStackTrace();
                                        psi = 360.0 ;
                                }
                        }

                        System.out.print(b.getPDBCode() + " " + b.getPDBName() + ":"  );

                        System.out.println(String.format("\tphi: %+7.2f psi: %+7.2f", phi, psi));

                }
    Since:
    1.4
    Version:
    %I% %G%
    Author:
    Andreas Prlic

    • Method Detail

      • clone

        Structure clone()
        Return an identical copy of this Structure object
        Returns:
        identical copy of this Structure object

      • setPDBCode

        void setPDBCode​(String pdb_id)
        Set PDB code of structure .
        Parameters:
        pdb_id - a String specifying the PDBCode
        See Also:
        getPDBCode()

      • setName

        void setName​(String name)
        Set biological name of Structure .
        Parameters:
        name - a String specifying the biological name of the Structure
        See Also:
        getName()

      • setStructureIdentifier

        void setStructureIdentifier​(StructureIdentifier structureIdentifier)
        Set the identifier corresponding to this structure
        Parameters:
        structureIdentifier - the structureIdentifier corresponding to this structure

      • size

        int size()
        Return number of polymer Chains in this Structure for first model.
        Returns:
        the number of polymer Chains in this Structure

      • size

        int size​(int modelnr)
        Return number of chains of model.
        Parameters:
        modelnr - an int specifying the number of the Model that should be used
        Returns:
        an int representing the number of Chains in this Model

      • nrModels

        int nrModels()
        Return the number of models . In this implementation also XRAY structures have "1 model", since model is the container for the chains. to test if a Structure is an NMR structure use isNmr().
        Returns:
        an int representing the number of models in this Structure
        See Also:
        isNmr()

      • isNmr

        boolean isNmr()
        Test if this structure is an NMR structure.
        Returns:
        true if this Structure has been solved by NMR
        See Also:
        nrModels()

      • isCrystallographic

        boolean isCrystallographic()
        Test if this structure is a crystallographic structure, i.e. it is an asymmetric unit from which it is possible to reconstruct the crystal lattice given cell parameters and space group.
        Returns:
        true if crystallographic, false otherwise

      • addModel

        void addModel​(List<Chain> model)
        Add a new model.
        Parameters:
        model - a List object containing the Chains of the new Model

      • setModel

        void setModel​(int position,
              List<Chain> model)
        A convenience function if one wants to edit and replace the models in a structure. Allows to set (replace) the model at position with the new List of Chains.
        Parameters:
        position - starting at 0
        model - list of chains representing a model

      • getModel

        List<Chain> getModel​(int modelnr)
        Retrieve all Chains belonging to a model .
        Parameters:
        modelnr - an int
        Returns:
        a List object containing the Chains of Model nr. modelnr
        See Also:
        getChains(int modelnr)

      • setChains

        void setChains​(List<Chain> chains)
        Set the chains of a structure, if this is a NMR structure, this will only set model 0.
        Parameters:
        chains - the list of chains for this structure.
        See Also:
        setChains(int, List)

      • getChains

        List<Chain> getChains​(int modelnr)
        Retrieve all chains of a model.
        Parameters:
        modelnr - an int
        Returns:
        a List object containing the Chains of Model nr. modelnr
        See Also:
        getModel(int)

      • setChains

        void setChains​(int modelnr,
               List<Chain> chains)
        Set the chains for a model
        Parameters:
        chains - the chains for a model
        modelnr - the number of the model

      • getPolyChains

        List<Chain> getPolyChains()
        Return all polymeric chains for the first model
        Returns:
        all polymeric chains.
        Since:
        5.0

      • getPolyChains

        List<Chain> getPolyChains​(int modelIdx)
        Return all polymeric chains for the given model index.
        Parameters:
        modelIdx - the model index
        Returns:
        all polymeric chains.
        Since:
        5.0

      • getNonPolyChains

        List<Chain> getNonPolyChains()
        Return all non-polymeric chains for the first model
        Returns:
        all non-polymeric chains.
        Since:
        5.0

      • getNonPolyChains

        List<Chain> getNonPolyChains​(int modelIdx)
        Return all non-polymeric chains for the given model index.
        Parameters:
        modelIdx - the model index
        Returns:
        all non-polymeric chains.
        Since:
        5.0

      • getWaterChains

        List<Chain> getWaterChains​(int modelIdx)
        Return all water chains for the given model index
        Parameters:
        modelIdx -
        Returns:
        Since:
        5.0

      • addChain

        void addChain​(Chain chain)
        Add a new chain to the first model
        Parameters:
        chain - a Chain object

      • addChain

        void addChain​(Chain chain,
              int modelnr)
        Add a new chain to the model specified by the given index
        Parameters:
        chain - a Chain object
        modelnr - an int specifying to which model the Chain should be added

      • getChainByIndex

        Chain getChainByIndex​(int chainIndex)
        Retrieve a chain by its index within the Structure .
        Parameters:
        chainIndex - the index of the desired chain in the structure
        Returns:
        a Chain object

      • getChainByIndex

        Chain getChainByIndex​(int modelnr,
                      int chainIndex)
        Retrieve a chain by its indices within the Structure and model.
        Parameters:
        chainIndex - the index of the desired chain in the structure
        modelnr - the model the desired chain is in
        Returns:
        a Chain object

      • hasChain

        boolean hasChain​(String asymId)
        Check if a chain with the chainId aymId is contained in this structure.
        Parameters:
        asymId - the Id of the chain
        Returns:
        true if a chain with the id asymId is found

      • hasNonPolyChain

        boolean hasNonPolyChain​(String asymId)
        Check if a non polymeric chain with chainId asymId is contained in the structure.
        Parameters:
        asymId - the id of the chain
        Returns:
        true if a nonpolymeric chain with the asymId is found
        Since:
        5.0

      • hasPdbChain

        boolean hasPdbChain​(String authId)
        Check if a chain with chain name authId is contained in the structure
        Parameters:
        authId - the chain name
        Returns:
        true if a chain with the name authId is found

      • findGroup

        Group findGroup​(String authId,
                String pdbResnum)
         throws StructureException
        Request a particular group from a structure. by default considers only the first model in the structure.
        Parameters:
        authId - the name of the chain to use
        pdbResnum - the PDB residue number of the requested group
        Returns:
        Group the requested Group
        Throws:
        StructureException

      • findGroup

        Group findGroup​(String authId,
                String pdbResnum,
                int modelnr)
         throws StructureException
        Request a particular group from a structure. considers only model nr X. count starts with 0.
        Parameters:
        authId - the chain name of the chain to use
        pdbResnum - the PDB residue number of the requested group
        modelnr - the number of the model to use
        Returns:
        Group the requested Group
        Throws:
        StructureException

      • getChainByPDB

        @Deprecated
Chain getChainByPDB​(String authId)
             throws StructureException
        Deprecated.
        use getPolyChainByPDB(String) instead
        Request a chain by its public id (author id) for the first model. Before 5.0 it returned a Chain that had both polymeric and non-polymeric groups following the PDB-file data model. Since 5.0 it only returns the polymeric part of the chain.
        Parameters:
        authId - the author id (chainName, public chain id)
        Returns:
        the Chain that matches the authId
        Throws:
        StructureException - if chain can't be found

      • getChainByPDB

        @Deprecated
Chain getChainByPDB​(String authId,
                    int modelIdx)
             throws StructureException
        Deprecated.
        use getPolyChainByPDB(String,int) instead
        Request a chain by its public id (author id) for the given model index. Before 5.0 it returned a Chain that had both polymeric and non-polymeric groups following the PDB-file data model. Since 5.0 it only returns the polymeric part of the chain.
        Parameters:
        authId - the author id (chainName, public chain id)
        modelIdx - the index of the required model (0-based)
        Returns:
        the Chain that matches the authId in the model
        Throws:
        StructureException - if chain can't be found

      • getPolyChain

        Chain getPolyChain​(String asymId)
        Retrieve a polymeric Chain based on the 'internal' chain id (asymId) for the first model

        See getPolyChainByPDB(String) for a similar method using the chain name (authId).

        Parameters:
        asymId - the asymId (chainId)
        Returns:
        a polymeric Chain or null if it can't be found
        Since:
        5.0

      • getPolyChain

        Chain getPolyChain​(String asymId,
                   int modelIdx)
        Retrieve a polymeric Chain based on the 'internal' chain id (asymId) for the given model index

        See getPolyChainByPDB(String, int) for a similar method using the chain name (authId).

        Parameters:
        asymId - the asymId (chainId)
        modelIdx - the index of the required model (0-based)
        Returns:
        a polymeric Chain or null if it can't be found
        Since:
        5.0

      • getPolyChainByPDB

        Chain getPolyChainByPDB​(String authId)
        Retrieve a polymeric Chain based on the 'public' chain name (authId) for the first model

        See getPolyChain(String) for a similar method using the chain id (asymId).

        Parameters:
        authId - the author id (chainName, public chain id)
        Returns:
        a polymeric Chain or null if it can't be found
        Since:
        5.0

      • getPolyChainByPDB

        Chain getPolyChainByPDB​(String authId,
                        int modelIdx)
        Retrieve a polymeric Chain based on the 'public' chain name (authId) for the given model index.

        See getPolyChain(String, int) for a similar method using the chain id (asymId).

        Parameters:
        authId - the author id (chainName, public chain id)
        modelIdx - the index of the required model (0-based)
        Returns:
        a polymeric Chain or null if it can't be found
        Since:
        5.0

      • getNonPolyChain

        Chain getNonPolyChain​(String asymId)
        Retrieve a non-polymeric Chain based on the 'internal' chain id (asymId) for the first model
        Parameters:
        asymId - the asymId (chainId)
        Returns:
        a non-polymeric chain or null if it can't be found
        Since:
        5.0

      • getNonPolyChain

        Chain getNonPolyChain​(String asymId,
                      int modelIdx)
        Retrieve a non-polymeric Chain based on the 'internal' chain id (asymId) for the given model index
        Parameters:
        asymId - the asymId (chainId)
        modelIdx - the index of the required model (0-based)
        Returns:
        a non-polymeric Chain or null if it can't be found
        Since:
        5.0

      • getNonPolyChainsByPDB

        List<Chain> getNonPolyChainsByPDB​(String authId)
        Retrieve all non-polymeric Chains corresponding to the given 'public' chain name (authId) for the first model.
        Parameters:
        authId - the author id (chainName, public chain id)
        Returns:
        a list of non-polymeric Chains, if none found the list will be empty
        Since:
        5.0

      • getNonPolyChainsByPDB

        List<Chain> getNonPolyChainsByPDB​(String authId,
                                  int modelIdx)
        Retrieve all non-polymeric Chains corresponding to the 'public' chain name (authId) and the given model index.
        Parameters:
        authId - the author id (chainName, public chain id)
        modelIdx - the index of the required model (0-based)
        Returns:
        a list of non-polymeric Chains, if none found the list will be empty
        Since:
        5.0

      • getWaterChain

        Chain getWaterChain​(String asymId)
        Retrieve a water Chain based on the 'internal' chain id (asymId) for the first model
        Parameters:
        asymId - the asymId (chainId)
        Returns:
        a water Chain or null if it can't be found
        Since:
        5.0

      • getWaterChain

        Chain getWaterChain​(String asymId,
                    int modelIdx)
        Retrieve a water chain based on the 'internal' chain id (asymId) for the given model index
        Parameters:
        asymId - the asymId (chainId)
        modelIdx - the index of the required model (0-based)
        Returns:
        Since:
        5.0

      • getWaterChainByPDB

        Chain getWaterChainByPDB​(String authId)
        Retrieve a water Chain based on the 'public' chain name (authId) for the first model
        Parameters:
        authId - the author id (chainName, public chain id)
        Returns:
        Since:
        5.0

      • getWaterChainByPDB

        Chain getWaterChainByPDB​(String authId,
                         int modelIdx)
        Retrieve a water Chain based on the 'public' chain name (authId) for the given model index
        Parameters:
        authId - the author id (chainName, public chain id)
        modelIdx - the index of the required model (0-based)
        Returns:
        Since:
        5.0

      • toPDB

        String toPDB()
        Create a String that contains this Structure's contents in PDB file format.
        Returns:
        a String that looks like a PDB file
        See Also:
        FileConvert

      • toMMCIF

        String toMMCIF()
        Create a String that contains this Structure's contents in MMCIF file format.
        Returns:
        a String representation of the Structure object in mmCIF.

      • setDBRefs

        void setDBRefs​(List<DBRef> dbrefs)
        Set the list of database references for this structure
        Parameters:
        dbrefs - list of DBRef objects

      • getDBRefs

        List<DBRef> getDBRefs()
        Get the list of database references
        Returns:
        list of DBRef objects

      • getEntityById

        EntityInfo getEntityById​(int entityId)
        Request a particular entity by its entity id (mol id in legacy PDB format)
        Parameters:
        entityId - the number of the entity
        Returns:
        an entity, or null if the molId was not found

      • getPDBHeader

        PDBHeader getPDBHeader()
        Return the header information for this PDB file
        Returns:
        the PDBHeader object

      • hasJournalArticle

        boolean hasJournalArticle()
        Return whether or not the entry has an associated journal article or ation. The JRNL section is not mandatory and thus may not be present.
        Returns:
        flag if a JournalArticle has been found.

      • getJournalArticle

        JournalArticle getJournalArticle()
        Get the associated publication as defined by the JRNL records in a PDB file.
        Returns:
        a JournalArticle

      • setJournalArticle

        void setJournalArticle​(JournalArticle journalArticle)
        Set the associated publication as defined by the JRNL records in a PDB file.
        Parameters:
        journalArticle - a JournalArticle object

      • getSSBonds

        List<Bond> getSSBonds()
        Get the list of disulfide Bonds as they have been defined in the PDB files
        Returns:
        a list of Bonds

      • setSSBonds

        void setSSBonds​(List<Bond> ssbonds)
        Set the list of SSBonds for this structure
        Parameters:
        ssbonds -

      • addSSBond

        void addSSBond​(Bond ssbond)
        Add a single disulfide Bond to this structure
        Parameters:
        ssbond - a disulfide bond

      • setPDBHeader

        void setPDBHeader​(PDBHeader header)
        Set the the header information for this PDB file
        Parameters:
        header - the PDBHeader object

      • getId

        Long getId()
        Get the ID used by Hibernate
        Returns:
        the ID used by Hibernate

      • setId

        void setId​(Long id)
        set the ID used by Hibernate
        Parameters:
        id - the id

      • setSites

        void setSites​(List<Site> sites)
        Parameters:
        sites - the sites to set in the structure

      • getSites

        List<Site> getSites()
        Returns:
        the sites contained in this structure

      • setBiologicalAssembly

        void setBiologicalAssembly​(boolean biologicalAssembly)
        Set a flag to indicate if this structure is a biological assembly
        Parameters:
        biologicalAssembly - true if biological assembly, otherwise false
        Since:
        3.2

      • isBiologicalAssembly

        boolean isBiologicalAssembly()
        Get flag that indicates if this structure is a biological assembly
        Returns:
        true if biological assembly, otherwise false
        Since:
        3.2

      • setCrystallographicInfo

        void setCrystallographicInfo​(PDBCrystallographicInfo crystallographicInfo)
        Set crystallographic information for this structure
        Parameters:
        crystallographicInfo - crystallographic information
        Since:
        3.2

      • resetModels

        void resetModels()
        Resets all models of this Structure
        Since:
        4.0.1

      • getPdbId

        @Deprecated
String getPdbId()
        Deprecated.
        From BioJava 4.2, use getPDBCode() or getStructureIdentifier().toCanonical().getPdbId()
        Returns the PDB identifier associated with this StructureIdentifier.

      • getRanges

        @Deprecated
List<String> getRanges()
        Deprecated.
        From BioJava 4.2, use getStructureIdentifier().toCanonical().getRanges()
        Returns a list of residue ranges. For example: 
         getRanges().get(0): 'A'
 getRanges().get(1): 'B_5-100'
        This is a unique representation.

      • getIdentifier

        String getIdentifier()
        Get a string representing this structure's contents. The following places are searched for a non-null value, with the first being returned:
        1. getStructureIdentifier().getIdentifier(), which should give the string originally used to create the structure
        2. getName()
        3. A combination of getPDBCode() with a heuristic description of the residue ranges, in SubstructureIdentifier format.
        Returns:
        A SubstructureIdentifier-format string describing the residue ranges in this structure
        Since:
        The behavior of this method changed in BioJava 4.2. Previously it returned the same value as getPDBCode()